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User:Jts1882/phylogeny/Fish Tree of Life

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The Fish Tree of Life project[1][2] provides downloadable Newick files for their order and family phylogenies. The cladograms on this page produced using the data in these files with the {{clade}} template and some regular expressions to trim the numerical information and add wikilinks.

Method

[edit]

Uses the {{clade}} template with the |newickX= parameter to provide a Newick string. The parameters |newickX-patternY= and |newickX-replaceY= specify a pattern with a replacement string for preprocess the Newick string (X represents the number of the Newick string, Y the number of the operation to apply to that string). The first pattern and replacement remove the numbers after the colon. The second adds a wikilink to the taxon name.

{{clade
|newick1-pattern1=:[%d]+%.[%d]+
|newick1-replace1=
|newick1-pattern2=([%a]+)
|newick1-replace2=[[%1]]
|newick1=FISH_TREE_OF_LIFE_DATA
}}

Example using the order data:

{{clade
|newick1-pattern1=:[%d]+%.[%d]+
|newick1-replace1=
|newick1-pattern2=([%a]+)
|newick1-replace2=[[%1]]
|newick1=(Polypteriformes:368.027041,(Acipenseriformes:333.36982,((Lepisosteiformes:251.2,Amiiformes:251.2):48.943209,((Elopiformes:165.843139,(Anguilliformes:146.0535,(Notacanthiformes:128.347636,Albuliformes:128.347637):17.705862):19.789641):26.939643,((Osteoglossiformes:169.672422,Hiodontiformes:169.672422):17.471963,((Alepocephaliformes:171.108487,(Clupeiformes:165.805142,(Gonorynchiformes:158.176817,(Cypriniformes:142.110586,(Gymnotiformes:124.40688,(Siluriformes:116.06004,Characiformes:116.060038):8.346838):17.703708):16.06623):7.628325):5.303345):6.36875,(Lepidogalaxiiformes:172.157387,((Argentiniformes:158.384449,(Salmoniformes:121.520222,Esociformes:121.520223):36.864226):7.145808,((Stomiatiformes:141.207619,Osmeriformes:141.207618):20.672626,(Galaxiiformes:158.157427,(Ateleopodiformes:149.146565,(Aulopiformes:146.049394,(Myctophiformes:141.995558,((Polymixiiformes:125.926727,(Percopsiformes:119.550085,(Zeiformes:112.30372,(Gadiformes:99.890622,Stylephoriformes:99.890622):12.413099):7.246364):6.376642):12.033509,(Lampridiformes:135.505912,((Beryciformes:124.850407,Holocentriformes:124.850408):4.793566,(Ophidiiformes:122.65368,(Batrachoidiformes:120.167471,((Labriformes:112.838678,((Tetraodontiformes:101.62039,Lophiiformes:101.620388):4.659797,((Acanthuriformes:96.101473,Ephippiformes:96.101474):7.010952,(Spariformes:99.425522,(Incertae_sedis_in_Eupercaria:96.331828,(Uranoscopiformes:92.977695,(Perciformes:92.028374,(Centrarchiformes:90.740466,Pempheriformes:90.740464):1.287908):0.949321):3.354133):3.093696):3.686903):3.167759):6.558493):3.243613,(((Gobiiformes:99.575295,Kurtiformes:99.575295):11.781977,(Syngnathiformes:108.599677,Scombriformes:108.599675):2.757596):3.029696,(((Anabantiformes:94.89388,Synbranchiformes:94.89388):13.184223,((Pleuronectiformes:79.610542,Incertae_sedis_in_Carangaria:79.610542):3.123197,(Carangiformes:75.53813,Istiophoriformes:75.538129):7.195608):25.344365):5.14771,(Mugiliformes:107.660061,(Incertae_sedis_in_Ovalentaria:106.091317,((Cichliformes:98.738035,Pholidichthyiformes:98.738035):6.170613,(Atheriniformes:98.599758,(Cyprinodontiformes:97.3635,Beloniformes:97.363501):1.236257):6.308891):1.182668):1.568745):5.565751):1.161156):1.695324):4.085179):2.48621):6.990293):5.861938):2.454324):4.035323):4.053834):3.097172):9.010861):3.722819):3.650012):6.62713):5.31985):9.667148):5.638398):107.360427):33.22661):34.657221);
}}

Order phylogeny

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;

Polypteriformes

:

Acipenseriformes

:
:

Lepisosteiformes

Amiiformes

:
:

Elopiformes

:

Anguilliformes

:

Notacanthiformes

Albuliformes

:
:

Osteoglossiformes

Hiodontiformes

:
:

Alepocephaliformes

:

Clupeiformes

:

Gonorynchiformes

:

Cypriniformes

:

Gymnotiformes

:

Siluriformes

Characiformes

:

Lepidogalaxiiformes

:
:

Argentiniformes

:

Salmoniformes

Esociformes

:
:

Stomiatiformes

Osmeriformes

:

Galaxiiformes

:

Ateleopodiformes

:

Aulopiformes

:

Myctophiformes

:
:

Polymixiiformes

:

Percopsiformes

:

Zeiformes

:

Gadiformes

Stylephoriformes

:

Lampridiformes

:
:

Beryciformes

Holocentriformes

:

Ophidiiformes

:

Batrachoidiformes

:
:

Labriformes

:
:

Tetraodontiformes

Lophiiformes

:
:

Acanthuriformes

Ephippiformes

:

Spariformes

:

Incertae sedis in Eupercaria

:

Uranoscopiformes

:

Perciformes

:

Centrarchiformes

Pempheriformes

:
:
:

Gobiiformes

Kurtiformes

:

Syngnathiformes

Scombriformes

:
:
:

Anabantiformes

Synbranchiformes

:
:

Pleuronectiformes

Incertae sedis in Carangaria

:

Carangiformes

Istiophoriformes

:

Mugiliformes

:

Incertae sedis in Ovalentaria

:
:

Cichliformes

Pholidichthyiformes

:

Atheriniformes

:

Cyprinodontiformes

Beloniformes

Family phylogeny

[edit]
;

Polypteridae

Acipenseridae

Polyodontidae

Lepisosteidae

Amiidae

Elopidae

Megalopidae

Halosauridae

Albulidae

Synaphobranchidae

Anguillidae

Serrivomeridae

Nemichthyidae

Moringuidae

Eurypharyngidae

Saccopharyngidae

Chlopsidae

Muraenidae

Heterenchelyidae

Derichthyidae

Colocongridae

Congridae

Ophichthidae

Muraenesocidae

Hiodontidae

Osteoglossidae

Notopteridae

Mormyridae

Gymnarchidae

Alepocephalidae

Platytroctidae

Denticipitidae

Chirocentridae

Clupeidae

Engraulidae

Gonorynchidae

Kneriidae

Chanidae

Cyprinidae

Catostomidae

Gyrinocheilidae

Botiidae

Vaillantellidae

Cobitidae

Ellopostomatidae

Nemacheilidae

Balitoridae

Sternopygidae

Hypopomidae

Apteronotidae

Gymnotidae

Rhamphichthyidae

Distichodontidae

Citharinidae

Crenuchidae

Lebiasinidae

Erythrinidae

Ctenoluciidae

Chalceidae

Characidae

Acestrorhynchidae

Iguanodectidae

Triportheidae

Bryconidae

Gasteropelecidae

Alestidae

Parodontidae

Chilodontidae

Cynodontidae

Serrasalmidae

Hemiodontidae

Anostomidae

Curimatidae

Prochilodontidae

Nematogenyidae

Trichomycteridae

Callichthyidae

Loricariidae

Scoloplacidae

Diplomystidae

Cetopsidae

Doradidae

Aspredinidae

Clariidae

Heteropneustidae

Siluridae

Chacidae

Bagridae

Horabagridae

Schilbeidae

Sisoridae

Amblycipitidae

Akysidae

Pangasiidae

Plotosidae

Pimelodidae

Claroteidae

Mochokidae

Malapteruridae

Ariidae

Anchariidae

Ictaluridae

Cranoglanididae

Lepidogalaxiidae

Salmonidae

Esocidae

Umbridae

Bathylagidae

Microstomatidae

Argentinidae

Opisthoproctidae

Retropinnidae

Osmeridae

Salangidae

Plecoglossidae

Gonostomatidae

Diplophidae

Stomiidae

Sternoptychidae

Phosichthyidae

Galaxiidae

Ateleopodidae

Pseudotrichonotidae

Paraulopidae

Synodontidae

Aulopidae

Giganturidae

Ipnopidae

Bathysauridae

Chlorophthalmidae

Scopelarchidae

Paralepididae

Notosudidae

Myctophidae

Neoscopelidae

Polymixiidae

Percopsidae

Amblyopsidae

Aphredoderidae

Macrouridae

Stylephoridae

Zenionidae

Parazenidae

Zeidae

Grammicolepididae

Oreosomatidae

Cyttidae

Veliferidae

Lamprididae

Lophotidae

Trachipteridae

Regalecidae

Holocentridae

Trachichthyidae

Melamphaidae

Berycidae

Stephanoberycidae

Rondeletiidae

Cetomimidae

Barbourisiidae

Ophidiidae

Bythitidae

Batrachoididae

Apogonidae

Kurtidae

Trichonotidae

Odontobutidae

Rhyacichthyidae

Eleotridae

Gobiidae

Thalasseleotrididae

Dactylopteridae

Aulostomidae

Syngnathidae

Centriscidae

Pegasidae

Fistulariidae

Callionymidae

Mullidae

Champsodontidae

Chiasmodontidae

Centrolophidae

Arripidae

Pomatomidae

Trichiuridae

Gempylidae

Scombridae

Icosteidae

Bramidae

Tetragonuridae

Stromateidae

Nomeidae

Ariommatidae

Mastacembelidae

Chaudhuriidae

Synbranchidae

Indostomidae

Badidae

Nandidae

Channidae

Osphronemidae

Anabantidae

Helostomatidae

Polynemidae

Toxotidae

Carangidae

Leptobramidae

Menidae

Istiophoridae

Xiphiidae

Centropomidae

Sphyraenidae

Lactariidae

Psettodidae

Citharidae

Pleuronectidae

Scophthalmidae

Achiridae

Soleidae

Samaridae

Rhombosoleidae

Bothidae

Poecilopsettidae

Mugilidae

Ambassidae

Pseudochromidae

Congrogadidae

Pomacentridae

Embiotocidae

Plesiopidae

Grammatidae

Opistognathidae

Gobiesocidae

Tripterygiidae

Blenniidae

Clinidae

Chaenopsidae

Labrisomidae

Polycentridae

Cichlidae

Pholidichthyidae

Atherinopsidae

Phallostethidae

Atherinidae

Melanotaeniidae

Bedotiidae

Isonidae

Adrianichthyidae

Exocoetidae

Hemiramphidae

Belonidae

Zenarchopteridae

Rivulidae

Nothobranchiidae

Aplocheilidae

Poeciliidae

Anablepidae

Cyprinodontidae

Fundulidae

Valenciidae

Goodeidae

Profundulidae

Labridae

Pempheridae

Glaucosomatidae

Lophiidae

Ogcocephalidae

Antennariidae

Chaunacidae

Gigantactinidae

Ceratiidae

Oneirodidae

Himantolophidae

Melanocetidae

Cepolidae

Triodontidae

Ostraciidae:49

Aracanidae

Molidae

Tetraodontidae

Diodontidae

Monacanthidae

Balistidae

Triacanthidae

Triacanthodidae

Ephippidae

Luvaridae

Acanthuridae

Zanclidae

Siganidae

Caproidae

Priacanthidae

Scatophagidae

Sciaenidae

Malacanthidae

Lethrinidae

Sparidae

Nemipteridae

Hapalogenyidae

Lobotidae

Chaetodontidae

Leiognathidae

Pomacanthidae

Haemulidae

Lutjanidae

Monodactylidae

Emmelichthyidae

Dinopercidae

Sillaginidae

Moronidae

Gerreidae

Centrogenyidae

Pinguipedidae

Uranoscopidae

Terapontidae

Kuhliidae

Kyphosidae

Oplegnathidae

Enoplosidae

Cheilodactylidae

Cirrhitidae

Percichthyidae

Sinipercidae

Centrarchidae

Elassomatidae

Pentacerotidae

Banjosidae

Lateolabracidae

Polyprionidae

Acropomatidae

Howellidae

Dinolestidae

Bathyclupeidae

Symphysanodontidae

Scombropidae

Epigonidae

Percophidae

Creediidae

Bembropidae

Trachinidae

Congiopodidae

Percidae

Niphonidae

Serranidae

Platycephalidae

Hoplichthyidae

Normanichthyidae

Sebastidae

Scorpaenidae

Tetrarogidae

Neosebastidae

Zanclorhynchidae

Triglidae

Peristediidae

Anoplopomatidae

Gasterosteidae

Hypoptychidae

Aulorhynchidae

Zaniolepididae

Bathymasteridae

Stichaeidae

Zoarcidae

Cryptacanthodidae

Zaproridae

Hexagrammidae

Trichodontidae

Liparidae

Cyclopteridae

Psychrolutidae

Cottidae

Jordaniidae

Agonidae

Scorpaenichthyidae

Ereuniidae

Rhamphocottidae

References

[edit]
  1. ^ Rabosky, Daniel L.; Chang, Jonathan; Title, Pascal O.; Cowman, Peter F.; Sallan, Lauren; Friedman, Matt; Kaschner, Kristin; Garilao, Cristina; Near, Thomas J.; Coll, Marta; Alfaro, Michael E. (2018). "An inverse latitudinal gradient in speciation rate for marine fishes". Nature. 559 (7714): 392–395. doi:10.1038/s41586-018-0273-1. ISSN 0028-0836.
  2. ^ Chang, Jonathan; Rabosky, Daniel L.; Smith, Stephen A.; Alfaro, Michael E.; Silvestro, Daniele (2019). "An R package and online resource for macroevolutionary studies using the ray‐finned fish tree of life". Methods in Ecology and Evolution. 10 (7): 1118–1124. doi:10.1111/2041-210X.13182. ISSN 2041-210X.